Lee Weathers (Kate Mara), a stern and self-contained young woman, is a risk-assessment specialist from a company that funds research projects devoted to creating artificial human beings. She is called in to investigate an incident involving one of their experiments. The company dispatches her to a remote location where one of the company’s most promising projects, a human hybrid called Morgan (Anya Taylor-Joy), has violently lashed out at one of the scientists, Dr. Kathy Grieff (Jennifer Jason Leigh), after having a “tantrum”, in which she stabbed her in the eye with a pen. Over dinner with the scientists, Lee (who is revealed to be fluent in Chinese) discusses a previous incident at Helsinki with the lead scientists Dr. Lui Cheng (Michelle Yeoh) and Dr. Simon Ziegler (Toby Jones), in which most of the team of scientists were killed.

After Morgan violently kills a psychologist, Dr. Alan Shapiro (Paul Giamatti), who taunted and provoked her in an interview, Lee realizes that Morgan is too unpredictable, especially given her enhanced intelligence and strength, and must be terminated. The scientists, who have raised Morgan from birth (five years ago, owing to her enhanced growth rate) have grown attached to her and cannot bring themselves to kill her. As Lee is about to do so, the scientists inject her with sedative and imprison her in the glass cell in which Morgan had been held. They plan to escape with Morgan, who instead kills them and kidnaps her favorite handler, Dr. Amy Menser (Rose Leslie). In the scientists’ house, Cheng is recording an apology for the failure of the experiment, in which she hints that they were attempting to develop a creation with more human emotions, only to find that the result was harder to control. It is also revealed that Morgan had “weaponized design parameters”. After she has finished, Morgan enters the room and suffocates her.